As recent headline-grabbing resignations by two federal government ministers attest, the issue of academic plagiarism is a higher-profile matter in Germany, and with bigger political stakes, than almost anywhere else. Both defence minister Karl-Theodor zu Guttenberg, who quit his post in 2011, and Annette Schavan, the minister for education and research who departed from chancellor Angela Merkel’s team in early 2013, were forced out in the wake of claims made by whistleblowers that parts of their doctoral theses had been plagiarised.

Unsurprisingly, revelations over these cases and others like them have prompted change in academia – although not necessarily the change you would expect.

Responding to urgent calls from the federal government to address the issue, the German Research Foundation (the Deutsche Forschungs-gemeinschaft, or DFG), a major research-funding organisation and the biggest of its kind in Europe, is altering its guidelines on the reporting of plagiarism – to state that universities should no longer investigate allegations solely on the basis of anonymous tip-offs.

The implications may be far-reaching, and some experts fear that the change will restrict the exposure of academic misconduct.

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Without academic researchers identifying the problematic borrowings, it seems clear that zu Guttenberg would not have (very reluctantly) acknowledged that large parts of his 2006 doctoral thesis in law for the University of Bayreuth in Bavaria were taken from uncredited sources. Bayreuth stripped zu Guttenberg of his PhD in 2011.

Similarly, the rescinding this year of Schavan’s 1980 doctorate from Heinrich Heine University of Düsseldorf came about because of revelations made via a crowdsourced website, VroniPlag Wiki, which claimed that her thesis contained large sections of unoriginal work.

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But when last month the DFG published revisions to its “academic code of practice”, in response to urgent calls from the federal and regional governments to tackle the situation, its course of action surprised many.

“From now on, we will no longer investigate allegations of plagiarism in doctoral theses on the basis of anonymous tips alone,” says Dorothee Dzwonnek, secretary general of the DFG.

Expanding on this, the DFG stipulates in its revised guidelines that “in future, so-called ‘whistle-blowers’ will no longer be able to precipitate official investigations unless they are prepared to let themselves be named”.

Once whistleblowers have revealed their identity, the DFG would treat this information in strict confidence during the investigation. But while the DFG sees such a compromise as a modus operandi for future proceedings, the German Rectors’ Conference (HRK), which drew up the original “code of good academic practice at German universities” in 1998 together with the DFG, remains sceptical.

Then, as now, the HRK preferred a system of checks and balances within universities, consisting of an independent ombudsmen committee with at least three members, to maintain good academic conduct and deal with suspected irregularities.

Under that system, those making complaints remain anonymous. “In particular,” say the original HRK recommendations from 1998, “those who make accusations public are in breach of [good academic] conduct as the ombudsmen’s investigations are no longer confidential”.

But DFG president Peter Strohschneider says he has reservations about those people who make anonymous allegations, especially when complaints become public.

He feels that it is essential to deter those whistleblowers who, he suggests, act out of spiteful motives, purely to harm colleagues’ reputations. Dzwonnek agrees that the DFG must ensure first and foremost that all anonymous complaints are being made by people “acting in good faith”.

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Meanwhile, universities up and down the country will be obliged to act on the funder’s new recommendations. The DFG, an independent body based in Bonn that is subsidised by the ��ä�Ի��� (states) as well as the federal government, supports research in a wide variety of fields through a combination of grant schemes, awards and funding programmes, making it a powerful player on the German academic stage.

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In the meantime, the cases of zu Guttenberg and Schavan are only the most high-profile instances of suspect doctoral qualifications brought to light via online scrutiny. VroniPlag Wiki is the successor to an earlier site, GuttenPlag Wiki, that aired many of the zu Guttenberg allegations; a crowdsourced resource that examines the extent of plagiarism in German doctoral theses, it includes academics among its contributors. Some contributors are anonymous (such as the user who kick-started the Schavan scandal), but others are open about their involvement. The resource is named after Veronica Saß, the daughter of Edmund Stoiber, former state premier of Bavaria. Indeed, her dissertation was the next one after zu Guttenberg’s to get a public going-over.

Like zu Guttenberg, she obtained a doctorate in law, in her case from the University of Konstanz in southern Germany. And, like zu Guttenberg, she was stripped of her title after an anonymous tip-off prompted the university examinations committee to subject her thesis to a thorough examination.

What’s more, her brother, Dominic Stoiber, was pilloried after an anonymous complaint to the University of Innsbruck in Austria. He, however, was more fortunate: despite a court ruling against him, he won on appeal and was allowed to keep his doctoral title.

VroniPlag Wiki also played a key role in claiming the scalp of Schavan, who told Suddeutsche Zeitung at the height of the zu Guttenberg scandal that she was “ashamed, and not just secretly” at the revelations over the defence minister.

But by February of this year her own doctoral dissertation, “Person and Conscience: Studies on the Conditions, Need and Requirements of Today’s Consciences”, would be declared “largely plagiarised”, and rescinded.

Schavan’s comeuppance was “tough, certainly”, says Stefan Weber, a media and plagiarism expert and author of the 2008 book Das Google-Copy-Paste Syndrom, who took a keen interest in the case.

“But don’t forget she was not just a politician but the federal minister for education and science; you expected high academic standards from her.”

Gerhard Dannemann, a professor of English law, British economy and politics at Humboldt University in Berlin and a member of the VroniPlag team that scrutinised Schavan’s doctoral thesis, says: “We ran thorough, painstaking checks on over a hundred sources.”

The team worked very carefully, since there was obviously so much at stake in Schavan’s case, Dannemann insists.

Four days after losing her PhD title, Schavan announced that she would contest the decision but resign as education minister, so as not to damage her party’s chances at the federal election this September. Merkel, the German leader, parted from her close political ally with “a heavy heart”.

An important change in the revisions made by the DFG to its guidelines is the recommendation to limit investigative proceedings against suspected fraudulent theses to a maximum of one year. “We feel this is realistic,” says Dzwonnek, “as proceedings tended to drag on for years in the past.” Critics fear an attempt to gag the public. And what of the universities? They are arming themselves against the plagiarists of the future by installing plagiarism detection software or, alternatively, by providing more comprehensive support for doctoral students.

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Whichever way individual higher education institutions choose to go, Germany’s university sector is struggling with the long shadow cast by the zu Guttenberg and Schavan scandals.